I am seeking to get married. My family spoke with another family and I spoke with their daughter. They seemed like a good family and we all liked each other.

I felt I was for the most part compatible with the girl, but I still was not sure so I did a 2 rakat prayer for Allah to help with my decision. I was still confused and prayed another 2 rakat prayer a couple of days later. In the end we did istikhara of Quran from a Sheikh and he said the istikhara was not good and that it would cause a lot of problems.

I heard of some people who do istikhara multiple times. Does it make sense to do this? What would you advise in my situation?

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The istikhra is seeking advice from Allah swt.
Going against is not forbidden however unpleasant consequences happen as many has experienced.
But if there is a sense that circumstances have changed or something has changed in the matter then one can retake the istikhra